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- PDB-1qmg: Acetohydroxyacid isomeroreductase complexed with its reaction pro... -

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Basic information

Entry
Database: PDB / ID: 1qmg
TitleAcetohydroxyacid isomeroreductase complexed with its reaction product dihydroxy-methylvalerate, manganese and ADP-ribose.
ComponentsACETOHYDROXY-ACID ISOMEROREDUCTASE
KeywordsOXIDOREDUCTASE / BRANCHED CHAIN AMINO ACID BIOSYNTHESIS / REACTION PRODUCT / MANGANESE / ADP-RIBOSE
Function / homology
Function and homology information


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / L-valine biosynthetic process / isoleucine biosynthetic process / NADPH binding / chloroplast / magnesium ion binding / protein homodimerization activity / mitochondrion
Similarity search - Function
Ketol-acid reductoisomerase, plant / Ketol-acid reductoisomerase, C-terminal / Ketol-acid reductoisomerase / Ketol-acid reductoisomerase, N-terminal / Ketol-acid reductoisomerase, C-terminal domain / Acetohydroxy acid isomeroreductase, NADPH-binding domain / KARI N-terminal domain profile. / KARI C-terminal domain profile. / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 ...Ketol-acid reductoisomerase, plant / Ketol-acid reductoisomerase, C-terminal / Ketol-acid reductoisomerase / Ketol-acid reductoisomerase, N-terminal / Ketol-acid reductoisomerase, C-terminal domain / Acetohydroxy acid isomeroreductase, NADPH-binding domain / KARI N-terminal domain profile. / KARI C-terminal domain profile. / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHORIBOSE / 2,3-DIHYDROXY-VALERIANIC ACID / : / Ketol-acid reductoisomerase, chloroplastic
Similarity search - Component
Biological speciesSPINACIA OLERACEA (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsThomazeau, K. / Dumas, R. / Halgand, F. / Douce, R. / Biou, V.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Structure of Spinach Acetohydroxyacid Isomeroreductase Complexed with its Product of Reaction Dihydroxy-Methylvalerate, Manganese and Adp-Ribose
Authors: Thomazeau, K. / Dumas, R. / Halgand, F. / Forest, E. / Douce, R. / Biou, V.
#1: Journal: Embo J. / Year: 1997
Title: The Crystal Structure of Plant Acetohydroxyacid Isomeroreductase Complexed with its Reaction Product Dihydroxymethylvalerate, Manganese and (Phospho)-Adp-Ribose
Authors: Biou, V. / Dumas, R. / Cohen-Addad, C. / Douce, R. / Job, D. / Pebay-Peyroula, E.
History
DepositionSep 28, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETOHYDROXY-ACID ISOMEROREDUCTASE
B: ACETOHYDROXY-ACID ISOMEROREDUCTASE
C: ACETOHYDROXY-ACID ISOMEROREDUCTASE
D: ACETOHYDROXY-ACID ISOMEROREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,88821
Polymers228,1824
Non-polymers3,70617
Water37,6332089
1
A: ACETOHYDROXY-ACID ISOMEROREDUCTASE
B: ACETOHYDROXY-ACID ISOMEROREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,99211
Polymers114,0912
Non-polymers1,9019
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: ACETOHYDROXY-ACID ISOMEROREDUCTASE
D: ACETOHYDROXY-ACID ISOMEROREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,89610
Polymers114,0912
Non-polymers1,8058
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)110.800, 61.200, 161.700
Angle α, β, γ (deg.)90.00, 95.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.0143, -0.4385, -0.8986), (-0.4284, -0.8094, 0.4018), (-0.9035, 0.3907, -0.1763)67.2672, 18.0489, 64.9308
2given(0.0151, -0.8062, 0.5914), (0.4327, -0.528, -0.7308), (0.9014, 0.2669, 0.3409)-23.5214, 27.7852, 24.4769
3given(-1, -0.0052, 0.0008), (-0.0043, 0.8889, 0.458), (-0.0031, 0.458, -0.8889)43.8764, -17.7246, 73.8336

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
ACETOHYDROXY-ACID ISOMEROREDUCTASE / KETO-ACID REDUCTOISOMERASE / ALPHA-KETO-BETA-HYDROXYLACIL REDUCTOISOMERASE


Mass: 57045.543 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SPINACIA OLERACEA (spinach) / Organelle: PLASTID / Plasmid: PKK223.3
Gene (production host): CDNA FROM ACETOHYDROXY ACID ISOMEROREDUCTASE
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q01292, ketol-acid reductoisomerase (NADP+)

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Non-polymers , 5 types, 2106 molecules

#2: Chemical
ChemComp-APX / 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHORIBOSE


Mass: 644.335 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H29N5O17P3
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-DMV / 2,3-DIHYDROXY-VALERIANIC ACID


Mass: 148.157 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2089 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE MATURE AMINO ACID SEQUENCE IS DEVOID OF SIGNAL PEPTIDE. THEREFORE, RESIDUE 72 IS THE N-TERMINAL ...THE MATURE AMINO ACID SEQUENCE IS DEVOID OF SIGNAL PEPTIDE. THEREFORE, RESIDUE 72 IS THE N-TERMINAL AMINO ACID.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 54 %
Crystal growpH: 7.2
Details: PROTEIN WAS CRYSTALLISED FROM 1.8 M AMMONIUM SULFATE IN 0.1 M TRIS-HCL AT PH 7.2 IN THE PRESENCE OF AHB, NADPH, AND MN2+.
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Dumas, R., (1994) J. Mol. Biol., 242, 578.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
220 mMHEPES-KOH1drop
32 Mammonium sulfate1reservoir
40.1 MTris-HCl1reservoir
1protein1drop0.020mg

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.984
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1996 / Details: 2 MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.6→26 Å / Num. obs: 299230 / % possible obs: 96.6 % / Redundancy: 2.9 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.054 / Net I/σ(I): 18.8
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 14.6 / Rsym value: 0.096 / % possible all: 96.6
Reflection
*PLUS
Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 96.6 % / Rmerge(I) obs: 0.096

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
MOSFLMdata reduction
SCALAdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YVE

1yve


Resolution: 1.6→10 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2603215.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: NCS RESTRAINTS HAVE BEEN APPLIED UNTIL THE R-FACTOR DROPPED TO A VALUE OF 0.200. THEN THEY WERE PROGRESSIVELY LOOSENED AND REMOVED BECAUSE THE RATIO BETWEEN THE NUMBER OF REFLECTIONS AND ...Details: NCS RESTRAINTS HAVE BEEN APPLIED UNTIL THE R-FACTOR DROPPED TO A VALUE OF 0.200. THEN THEY WERE PROGRESSIVELY LOOSENED AND REMOVED BECAUSE THE RATIO BETWEEN THE NUMBER OF REFLECTIONS AND NUMBER OF DEGREES OF FREEDOM MADE IT POSSIBLE.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 13878 5 %RANDOM
Rwork0.196 ---
obs0.196 276291 97 %-
Displacement parametersBiso mean: 16.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15718 0 213 2089 18020
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.121.5
X-RAY DIFFRACTIONx_mcangle_it1.772
X-RAY DIFFRACTIONx_scbond_it1.582
X-RAY DIFFRACTIONx_scangle_it2.392.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 2207 5 %
Rwork0.245 42338 -
obs--94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3LIGAND.PARLIGAND.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.193 / Rfactor Rfree: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.55
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.94

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